Signatures within the esophageal microbiome are associated with host genetics, age, and disease
Experiment 1
Subjects
- Location of subjects
- Australia
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Esophagus Gullet,Oesophagus,Esophagus,esophagus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Esophageal adenocarcinoma adenocarcinoma - esophagus,adenocarcinoma of esophagus,adenocarcinoma of the esophagus,esophageal adenocarcinoma,esophagus adenocarcinoma,oesophageal adenocarcinoma,Esophageal adenocarcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cluster 1
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cluster 2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by Streptococcus (Streptococcus mitis/oralis/pneumoniae).
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Additional file 1, page 6
Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.
Abundance in Group 1: increased abundance in Cluster 2
NCBI | Quality Control | Links |
---|---|---|
Bacilli | ||
Lactobacillales | ||
Porphyromonas | ||
Prevotella | ||
Streptococcaceae | ||
Streptococcus | ||
unclassified Bacillales |
Revision editor(s): Fiddyhamma, Victoria
Signature 2
Source: Additional file 1, page 6
Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.
Abundance in Group 1: decreased abundance in Cluster 2
NCBI | Quality Control | Links |
---|---|---|
Prevotella |
Revision editor(s): Fiddyhamma, Victoria
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cluster 3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Additional file 1, page 6
Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.
Abundance in Group 1: increased abundance in Cluster 3
Revision editor(s): Fiddyhamma, Victoria
Signature 2
Source: Additional file 1, page 6
Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.
Abundance in Group 1: decreased abundance in Cluster 3
NCBI | Quality Control | Links |
---|---|---|
Prevotella |
Revision editor(s): Fiddyhamma, Victoria
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cluster 2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Additional file 1, page 6
Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.
Abundance in Group 1: increased abundance in Cluster 3
Revision editor(s): Fiddyhamma, Victoria
Signature 2
Source: Additional file 1, page 6
Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.
Abundance in Group 1: decreased abundance in Cluster 3
NCBI | Quality Control | Links |
---|---|---|
Bacilli | ||
Lactobacillales | ||
Porphyromonas | ||
Prevotella | ||
Streptococcaceae | ||
Streptococcus | ||
unclassified Bacillales |
Revision editor(s): Fiddyhamma, Victoria
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cluster 1
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cluster 2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by Streptococcus (Streptococcus mitis/oralis/pneumoniae).
Lab analysis
- Sequencing type
- WMS
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Additional file 1, page 7
Description: The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.
Abundance in Group 1: increased abundance in Cluster 2
NCBI | Quality Control | Links |
---|---|---|
Bacilli |
Revision editor(s): Fiddyhamma, Victoria
Signature 2
Source: Additional file 1, page 7
Description: The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.
Abundance in Group 1: decreased abundance in Cluster 2
Revision editor(s): Fiddyhamma, Victoria
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cluster 3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Additional file 1, page 7
Description: The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.
Abundance in Group 1: increased abundance in Cluster 3
NCBI | Quality Control | Links |
---|---|---|
Bacteroidales | ||
Bacteroidia | ||
Negativicutes | ||
Prevotella histicola | ||
Prevotella pallens | ||
Prevotella veroralis | ||
Selenomonadales | ||
Veillonella | ||
Veillonellaceae | ||
unclassified Veillonella |
Revision editor(s): Fiddyhamma, Victoria
Signature 2
Source: Additional file 1, page 7
Description: The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.
Abundance in Group 1: decreased abundance in Cluster 3
Revision editor(s): Fiddyhamma, Victoria
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cluster 2
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Additional file 1, page 7
Description: The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.
Abundance in Group 1: increased abundance in Cluster 3
NCBI | Quality Control | Links |
---|---|---|
Bacteroidales | ||
Bacteroidia | ||
Negativicutes | ||
Prevotella histicola | ||
Prevotella pallens | ||
Prevotella veroralis | ||
Selenomonadales | ||
Veillonella | ||
Veillonellaceae | ||
unclassified Veillonella |
Revision editor(s): Fiddyhamma, Victoria
Signature 2
Source: Additional file 1, page 7
Description: The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.
Abundance in Group 1: decreased abundance in Cluster 3
NCBI | Quality Control | Links |
---|---|---|
Bacilli |
Revision editor(s): Fiddyhamma, Victoria
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gastroesophageal reflux disease acid reflux,Esophageal Reflux,Gastresophageal reflux,Gastro Esophageal Reflux,Gastro oesophageal Reflux,Gastro-Esophageal Reflux,gastro-esophageal reflux,Gastro-oesophageal Reflux,Gastroesophageal Reflux,gastroesophageal reflux,GASTROESOPHAGEAL REFLUX DIS,gastroesophageal reflux disease,gastroesophageal reflux, pediatric,ger,GERD,GERD - gastro-esophageal reflux disease,Reflux, Gastro-Esophageal,Reflux, Gastro-oesophageal,Reflux, Gastroesophageal,Gastroesophageal reflux disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal (Normal esophagus)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GERD (Gastroesophageal reflux disease)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of patients with Gastroesophageal reflux disease.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 59
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
Signature 1
Source: Additional file 3, page 4
Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).
Abundance in Group 1: increased abundance in GERD (Gastroesophageal reflux disease)
NCBI | Quality Control | Links |
---|---|---|
Acetoanaerobium | ||
Filifactor | ||
unclassified Flavobacteriaceae | ||
Campylobacter |
Revision editor(s): Fiddyhamma, Victoria
Signature 2
Source: Additional file 3, page 4
Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).
Abundance in Group 1: decreased abundance in GERD (Gastroesophageal reflux disease)
NCBI | Quality Control | Links |
---|---|---|
Lactobacillus | ||
Enterobacteriaceae | ||
Enterobacterales | ||
Escherichia/Shigella sp. |
Revision editor(s): Victoria, Fiddyhamma
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Gastroesophageal reflux disease GERD(within subjects classified as PPI NO)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of patients with Gastroesophageal reflux disease(within subjects classified as PPI NO)
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
Signature 1
Source: Additional file 3, page 4
Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).
Abundance in Group 1: increased abundance in Gastroesophageal reflux disease GERD(within subjects classified as PPI NO)
Revision editor(s): Fiddyhamma
Signature 2
Source: Additional file 3, page 4
Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).
Abundance in Group 1: decreased abundance in Gastroesophageal reflux disease GERD(within subjects classified as PPI NO)
Revision editor(s): Fiddyhamma
Experiment 9
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Barrett's esophagus (ulcerative esophagitis) or (Barrett's esophagus),adenocarcinoma of esophagus,Barrett Epithelium,Barrett Esophagus,Barrett esophagus,Barrett metaplasia,Barrett Syndrome,Barrett's esophagus,Barrett's esophagus (disorder),Barrett's esophagus (disorder) [Ambiguous],Barrett's esophagus with esophagitis,Barrett's esophagus with esophagitis (disorder),Barrett's oesophagus,Barrett's Syndrome,Barrett's ulcer of esophagus,Barrett's ulcer of esophagus (disorder),Barretts Esophagus,Barretts syndrome,BE,cello,CLE,columnar epithelial-lined Lower esophagus,columnar-lined esophagus,Epithelium, Barrett,Esophagus, Barrett,Esophagus, Barrett's,Syndrome, Barrett,Syndrome, Barrett's,ulcerative esophagitis,barrett's esophagus
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Barrett’s Esophagus (BE)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of patients with Barrett’s Esophagus
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
Lab analysis
Statistical Analysis
Signature 1
Source: Additional file 3, page 4
Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).
Abundance in Group 1: increased abundance in Barrett’s Esophagus (BE)
NCBI | Quality Control | Links |
---|---|---|
Leptotrichia | ||
Capnocytophaga |
Revision editor(s): Fiddyhamma
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Gastroesophageal reflux disease (GERD)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
Lab analysis
Statistical Analysis
Signature 1
Source: Additional file 3, page 4
Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).
Abundance in Group 1: increased abundance in Barrett’s Esophagus (BE)
NCBI | Quality Control | Links |
---|---|---|
Burkholderiales | ||
Capnocytophaga |
Revision editor(s): Fiddyhamma
Signature 2
Source: Additional file 3, page 4
Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).
Abundance in Group 1: decreased abundance in Barrett’s Esophagus (BE)
NCBI | Quality Control | Links |
---|---|---|
Alloprevotella |
Revision editor(s): Fiddyhamma
Experiment 11
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Esophageal adenocarcinoma adenocarcinoma - esophagus,adenocarcinoma of esophagus,adenocarcinoma of the esophagus,esophageal adenocarcinoma,esophagus adenocarcinoma,oesophageal adenocarcinoma,Esophageal adenocarcinoma
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Glandular mucosa (GM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of patients with Glandular mucosa
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
Statistical Analysis
Signature 1
Source: Additional file 3, page 4
Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).
Abundance in Group 1: increased abundance in Glandular mucosa (GM)
NCBI | Quality Control | Links |
---|---|---|
Enterobacteriaceae | ||
Enterobacterales | ||
Prevotella | ||
Saccharofermentans |
Revision editor(s): Fiddyhamma
Signature 2
Source: Additional file 3, page 4
Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).
Abundance in Group 1: decreased abundance in Glandular mucosa (GM)
NCBI | Quality Control | Links |
---|---|---|
Prevotella | ||
Acetoanaerobium | ||
unclassified Prevotellaceae | ||
unclassified Veillonellaceae |
Revision editor(s): Fiddyhamma
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal
- Group 0 sample size Number of subjects in the control (unexposed) group
- 59
Lab analysis
Statistical Analysis
Signature 1
Source: Additional file 3, page 4
Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).
Abundance in Group 1: increased abundance in Glandular mucosa (GM)
NCBI | Quality Control | Links |
---|---|---|
Prevotella | ||
unclassified Prevotellaceae |
Revision editor(s): Fiddyhamma
Signature 2
Source: Additional file 3, page 4
Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).
Abundance in Group 1: decreased abundance in Glandular mucosa (GM)
NCBI | Quality Control | Links |
---|---|---|
unclassified Prevotellaceae | ||
unclassified Veillonellaceae |
Revision editor(s): Fiddyhamma
Experiment 13
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gastroesophageal reflux disease acid reflux,Esophageal Reflux,Gastresophageal reflux,Gastro Esophageal Reflux,Gastro oesophageal Reflux,Gastro-Esophageal Reflux,gastro-esophageal reflux,Gastro-oesophageal Reflux,Gastroesophageal Reflux,gastroesophageal reflux,GASTROESOPHAGEAL REFLUX DIS,gastroesophageal reflux disease,gastroesophageal reflux, pediatric,ger,GERD,GERD - gastro-esophageal reflux disease,Reflux, Gastro-Esophageal,Reflux, Gastro-oesophageal,Reflux, Gastroesophageal,Gastroesophageal reflux disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal (Normal esophagus)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GERD (Gastroesophageal reflux disease)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of patients with Gastroesophageal reflux disease.
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
Signature 1
Source: Additional file 3, page 5
Description: The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).
Abundance in Group 1: increased abundance in GERD (Gastroesophageal reflux disease)
NCBI | Quality Control | Links |
---|---|---|
Prevotella intermedia | ||
Prevotella micans | ||
Fusobacteriia | ||
Fusobacteriales | ||
Neisseria macacae | ||
Neisseria meningitidis | ||
Haemophilus parainfluenzae | ||
Treponema medium |
Revision editor(s): Fiddyhamma
Experiment 14
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GERD (Gastroesophageal reflux disease)within subjects classified as PPI NO
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of patients with Gastroesophageal reflux disease(within subjects classified as PPI NO)
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
Signature 1
Source: Additional file 3, page 5
Description: The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).
Abundance in Group 1: increased abundance in GERD (Gastroesophageal reflux disease)within subjects classified as PPI NO
NCBI | Quality Control | Links |
---|---|---|
Neisseria meningitidis |
Revision editor(s): Fiddyhamma
Signature 2
Source: Additional file 3, page 5
Description: The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).
Abundance in Group 1: decreased abundance in GERD (Gastroesophageal reflux disease)within subjects classified as PPI NO
NCBI | Quality Control | Links |
---|---|---|
Megasphaera micronuciformis | ||
Megasphaera | ||
Prevotella pallens | ||
rothia unclassifiedrothia unclassified |
Revision editor(s): Fiddyhamma
Experiment 15
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Barrett's esophagus (ulcerative esophagitis) or (Barrett's esophagus),adenocarcinoma of esophagus,Barrett Epithelium,Barrett Esophagus,Barrett esophagus,Barrett metaplasia,Barrett Syndrome,Barrett's esophagus,Barrett's esophagus (disorder),Barrett's esophagus (disorder) [Ambiguous],Barrett's esophagus with esophagitis,Barrett's esophagus with esophagitis (disorder),Barrett's oesophagus,Barrett's Syndrome,Barrett's ulcer of esophagus,Barrett's ulcer of esophagus (disorder),Barretts Esophagus,Barretts syndrome,BE,cello,CLE,columnar epithelial-lined Lower esophagus,columnar-lined esophagus,Epithelium, Barrett,Esophagus, Barrett,Esophagus, Barrett's,Syndrome, Barrett,Syndrome, Barrett's,ulcerative esophagitis,barrett's esophagus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Barrett’s Esophagus (BE)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of patients with Barrett’s Esophagus
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
Lab analysis
Statistical Analysis
Signature 1
Source: Additional file 3, page 5
Description: The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).
Abundance in Group 1: increased abundance in Barrett’s Esophagus (BE)
NCBI | Quality Control | Links |
---|---|---|
unclassified Gemella | ||
Streptococcus sanguinis | ||
Veillonella sp. oral taxon 780 |
Revision editor(s): Fiddyhamma
Experiment 16
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Esophageal adenocarcinoma adenocarcinoma - esophagus,adenocarcinoma of esophagus,adenocarcinoma of the esophagus,esophageal adenocarcinoma,esophagus adenocarcinoma,oesophageal adenocarcinoma,Esophageal adenocarcinoma
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Glandular mucosa (GM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of patients with Glandular mucosa
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
Statistical Analysis
Signature 1
Source: Additional file 3, page 5
Description: The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).
Abundance in Group 1: increased abundance in Glandular mucosa (GM)
Revision editor(s): Fiddyhamma
Experiment 17
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- GERD(Gastroesophageal reflux disease)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
Lab analysis
Statistical Analysis
Signature 1
Source: Additional file 3, page 5
Description: The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).
Abundance in Group 1: increased abundance in Glandular mucosa (GM)
Revision editor(s): Fiddyhamma
Experiment 18
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gastroesophageal reflux disease acid reflux,Esophageal Reflux,Gastresophageal reflux,Gastro Esophageal Reflux,Gastro oesophageal Reflux,Gastro-Esophageal Reflux,gastro-esophageal reflux,Gastro-oesophageal Reflux,Gastroesophageal Reflux,gastroesophageal reflux,GASTROESOPHAGEAL REFLUX DIS,gastroesophageal reflux disease,gastroesophageal reflux, pediatric,ger,GERD,GERD - gastro-esophageal reflux disease,Reflux, Gastro-Esophageal,Reflux, Gastro-oesophageal,Reflux, Gastroesophageal,Gastroesophageal reflux disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal (Cluster 1)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GERD(Gastroesophageal reflux disease) (Cluster 1)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of patients with Gastroesophageal reflux disease.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
- Sequencing type
- 16S
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Source: Additional file 3, page 6
Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis
Abundance in Group 1: increased abundance in GERD(Gastroesophageal reflux disease) (Cluster 1)
NCBI | Quality Control | Links |
---|---|---|
unclassified Flavobacteriaceae | ||
Streptococcus | ||
Veillonella |
Revision editor(s): Fiddyhamma
Signature 2
Source: Additional file 3, page 6
Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis
Abundance in Group 1: decreased abundance in GERD(Gastroesophageal reflux disease) (Cluster 1)
NCBI | Quality Control | Links |
---|---|---|
Lactobacillus | ||
Enterobacteriaceae | ||
Enterobacterales |
Revision editor(s): Fiddyhamma
Experiment 19
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal (Cluster 2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GERD(Gastroesophageal reflux disease) (Cluster 2)
Lab analysis
Statistical Analysis
Signature 1
Source: Additional file 3, page 6
Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis
Abundance in Group 1: increased abundance in GERD(Gastroesophageal reflux disease) (Cluster 2)
Revision editor(s): Fiddyhamma
Signature 2
Source: Additional file 3, page 6
Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis
Abundance in Group 1: decreased abundance in GERD(Gastroesophageal reflux disease) (Cluster 2)
NCBI | Quality Control | Links |
---|---|---|
Prevotella | ||
Gammaproteobacteria | ||
Pasteurellales | ||
Pasteurellaceae | ||
unclassified Pasteurellaceae |
Revision editor(s): Fiddyhamma
Experiment 20
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal (Cluster 3)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GERD(Gastroesophageal reflux disease) (Cluster 3)
Lab analysis
Statistical Analysis
Signature 1
Source: Additional file 3, page 6
Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis
Abundance in Group 1: increased abundance in GERD(Gastroesophageal reflux disease) (Cluster 3)
NCBI | Quality Control | Links |
---|---|---|
Prevotella | ||
Flavobacteriia | ||
Flavobacteriales | ||
Flavobacteriaceae | ||
Capnocytophaga | ||
unclassified Flavobacteriaceae | ||
unclassified Pseudomonadaceae | ||
unclassified Bacillota |
Revision editor(s): Fiddyhamma
Signature 2
Source: Additional file 3, page 6
Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis
Abundance in Group 1: decreased abundance in GERD(Gastroesophageal reflux disease) (Cluster 3)
NCBI | Quality Control | Links |
---|---|---|
Peptostreptococcaceae | ||
unclassified sequences |
Revision editor(s): Fiddyhamma
Experiment 21
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal (Cluster 1)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GERD(Gastroesophageal reflux disease) (Cluster 1)
Signature 1
Source: Additional file 3, page 7
Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis
Abundance in Group 1: increased abundance in GERD(Gastroesophageal reflux disease) (Cluster 1)
NCBI | Quality Control | Links |
---|---|---|
Alloprevotella tannerae | ||
unclassified Alloprevotella | ||
Eubacteriaceae | ||
Eubacterium |
Revision editor(s): Fiddyhamma
Signature 2
Source: Additional file 3, page 7
Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis
Abundance in Group 1: decreased abundance in GERD(Gastroesophageal reflux disease) (Cluster 1)
NCBI | Quality Control | Links |
---|---|---|
Alloprevotella |
Revision editor(s): Fiddyhamma
Experiment 22
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal (Cluster 2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GERD(Gastroesophageal reflux disease) (Cluster 2)
Lab analysis
Statistical Analysis
Signature 1
Source: Additional file 3, page 7
Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis
Abundance in Group 1: increased abundance in GERD(Gastroesophageal reflux disease) (Cluster 2)
Revision editor(s): Fiddyhamma
Signature 2
Source: Additional file 3, page 7
Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis
Abundance in Group 1: decreased abundance in GERD(Gastroesophageal reflux disease) (Cluster 2)
NCBI | Quality Control | Links |
---|---|---|
Haemophilus parahaemolyticus |
Revision editor(s): Fiddyhamma
Experiment 23
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal (Cluster 3)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GERD(Gastroesophageal reflux disease) (Cluster 3)
Lab analysis
Statistical Analysis
Signature 1
Source: Additional file 3, page 7
Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis
Abundance in Group 1: increased abundance in GERD(Gastroesophageal reflux disease) (Cluster 3)
Revision editor(s): Fiddyhamma
Signature 2
Source: Additional file 3, page 7
Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis
Abundance in Group 1: decreased abundance in GERD(Gastroesophageal reflux disease) (Cluster 3)
NCBI | Quality Control | Links |
---|---|---|
Prevotellaceae | ||
Bacteroidales | ||
Bacteroidia | ||
Atopobium | ||
Coriobacteriaceae | ||
Prevotella | ||
Coriobacteriales | ||
Lancefieldella parvula |
Revision editor(s): Fiddyhamma
Experiment 24
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Esophageal adenocarcinoma adenocarcinoma - esophagus,adenocarcinoma of esophagus,adenocarcinoma of the esophagus,esophageal adenocarcinoma,esophagus adenocarcinoma,oesophageal adenocarcinoma,Esophageal adenocarcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Subjects with normal esophagus on PPI-No
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Subjects with normal esophagus on PPI-Yes
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of patients with normal esophagus
Signature 1
Source: Additional figure 3 A
Description: Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI
Abundance in Group 1: increased abundance in Subjects with normal esophagus on PPI-Yes
NCBI | Quality Control | Links |
---|---|---|
Prevotella dentalis | ||
Streptococcus vestibularis |
Revision editor(s): Fiddyhamma
Signature 2
Source: Additional figure 3A
Description: Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI
Abundance in Group 1: decreased abundance in Subjects with normal esophagus on PPI-Yes
NCBI | Quality Control | Links |
---|---|---|
Peptostreptococcus | ||
Haemophilus influenzae | ||
Segatella salivae |
Revision editor(s): Fiddyhamma
Experiment 25
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Subjects with GERD on PPI-No
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Subjects with GERD on PPI-Yes
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of patients with gastroesophageal reflux disease
Lab analysis
Statistical Analysis
Signature 1
Source: Additional figure 3A
Description: Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI
Abundance in Group 1: increased abundance in Subjects with GERD on PPI-Yes
Revision editor(s): Fiddyhamma
Signature 2
Source: Additional figure 3A
Description: Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI
Abundance in Group 1: decreased abundance in Subjects with GERD on PPI-Yes
NCBI | Quality Control | Links |
---|---|---|
Neisseria meningitidis |
Revision editor(s): Fiddyhamma
Contents
- 1 Experiment 1
- 2 Experiment 2
- 3 Experiment 3
- 4 Experiment 4
- 5 Experiment 5
- 6 Experiment 6
- 7 Experiment 7
- 8 Experiment 8
- 9 Experiment 9
- 10 Experiment 10
- 11 Experiment 11
- 12 Experiment 12
- 13 Experiment 13
- 14 Experiment 14
- 15 Experiment 15
- 16 Experiment 16
- 17 Experiment 17
- 18 Experiment 18
- 19 Experiment 19
- 20 Experiment 20
- 21 Experiment 21
- 22 Experiment 22
- 23 Experiment 23
- 24 Experiment 24
- 25 Experiment 25